Format and Time
- Bioinformatics special lecture
- 9 ECTS credit points
- Lecture and programming projects (V4 Ü2)
- Course language: English
- The lecture will be held Wednesdays and Fridays 8:30 to 10:00 between October 15th, 2025 and February 4th, 2026 (in presence).
- First lecture: October 15th, 2025
- First tutorial: October 21st, 2025
Lecturers and TAs
- Jun.-Prof. Dr. Fabian Müller
- Dr. Friederike Grandke
- Irem Gündüz
- Nima Amini
- Adam Ashkar Masarwa
Course outline
The course reviews current technologies, laboratory techniques and bioinformatics methods for single-cell analysis. The lecture provides the theoretical background on single-cell *omics. Three programming projects will apply the learned bioinformatics methods to real-world single-cell datasets and will ensure that students have a working knowledge with practical experience on the material.
Content
Current technologies, laboratory techniques and bioinformatics methods for:
- Single-cell transcriptomics
- Single-cell epigenomics, including chromatin accessibility, DNA methylation and regulatory protein profiling
- Spatial transcriptomics
- Single-cell DNA sequencing
- Single-cell proteomics
- Single-cell multiomics
- Single-molecule sequencing
- Perturbation experiments with single-cell readout
- Emerging technologies
- Clinical Applications
Bioinformatics focus:
- Processing of single-cell sequencing data
- Data quality control
- Exploratory data analysis
- Differential data analysis
- Single-cell trajectory inference
- Data integration (multi-dataset and multi-omics)
- Inference of gene-regulation and gene regulatory networks
- Machine Learning & AI
Schedule
- Lectures:
- Wednesdays, 8:30-10:00, building E1.3, HS 003
- Fridays, 8:30-10:00, building E2.1, Room 001
- Tutorials:
- Tuesdays, 10:00-12:00, building E2.1, Room 001
- Programming assignments:
- Assignment 1 deadline: November 23rd, 2025
- Assignment 2 deadline: December 21st, 2025
- Assignment 3 deadline: January 25th, 2026
- Exam: February 4th, 2026
All Lectures will be held in presence.
Entrance requirements
To enroll, students should have a basic knowledge in Next Generation Sequencing (NGS), modern genomics and epigenomics, sequence analysis, linear algebra and machine learning. They should have basic skills for script-based programming using the R language.
Assessment/Exams
Final exam: written or oral, depending on participant numbers Participants need to score 50% on the three programming assignments to be admitted to the exam. The final grade will be based on the exam
What can you do to prepare for the lecture?
- Refresh your knowledge on Next-Generation Sequencing technology, genomics and epigenomics
- Refresh your knowledge on bioinformatics for sequence analysis, linear algebra and machine learning
- Familiarize yourself with the R programming language. You might find these tutorials useful:
Sign up
Deadline: October 19, 2025
If interested, sign up by submitting the following information via email to: irgu00001@stud.uni-saarland.de AND fabian.mueller@uni-saarland.de
- Your name
- Your UNIVERSITY email address
- Your field of study (e.g. Bioinformatics)
- Your current semester
- Your immatriculation number
Example:
TO: irgu00001@stud.uni-saarland.de, fabian.mueller@uni-saarland.de
SUBJECT: SCB (WiSe2025)
BODY: John Snow, jsnow@uni-saarland.de, Bioinformatics Master, 3, 999999
Lecture materials
Lecture slides, programming assignments and current research papers on single-cell technology and bioinformatics methods can be found on the lecture materials page (password protected)